When we went to Exch 2010, we only did the schema extension at the forest root and not at the child domains. We are about to go to Exch 2016. As we have some mailboxes in a couple of our child domains, can we do the /preparealldomains if some of the child domains didn’t get extended to 2010? Thanks for your reply.

There is only one schema master DC in the whole forest which exist in the root domain so we just need to update this DC. So you are fine with it.
Next 2 commands are required after this.

Required at the root domain – .\setup.exe /PrepareAD /IAcceptExchangeServerLicenseTerms /OrganizationName:orgname
Then you have 2 choice
Either run this in every domain – .\setup.exe /PrepareDomain /IAcceptExchangeServerLicenseTerms
or
Run this command at the root domain to update all domain -.\setup.exe /PrepareAllDomains /IAcceptExchangeServerLicenseTerms

All went well for me but I did see an Event log entry referencing a connection being made to a GC when I had teh replication link down. After I reenabled the replication a number of the site links were rebuilt by the KCC.

Also wondering if its overkill to disable replication when doing setup /PrepAD

Disabling replication was suggested to one of my premiere customer in Australia by Microsoft where the customer was following a practice of isolating a schema master.
Many organization’s security policies do not allow to update schema without isolating domain controller and if you remove the network cable or disable NIC then some of the prechecks will not complete.

I don’t see any harm in disabling replication of schema master during schema update. You can permanently remove this DC from the network if schema update corrupts the active directory.

I would respectfully ignore the blog shared by this Microsoft PFE because there is no reasoning provided.